What is the difference / relationship between GitHub Projects and Milestones?

The recent update to GitHub added something called Projects into the GitHub workflow, and because I don't have any particular experience with project tracking tools such as Jira or Trello (hey, at least I noticed the similarity), could anyone, please, elaborate on the (key) differences between GitHub's Milestones and the new Projects?

If I understand correctly, Milestones are a way of organizing issues into smaller "sub-projects" - smaller than the whole "project" (which, in my world view, is represented by the repository). When all issues are done/closed, the milestone can be regarded as complete.

The newly introduced Projects are also, as I see it, a way of organizing issues into smaller-than-the-repository "sub-projects" (albeit called Projects). I understand the workflow is supposed to be slightly different and more fine-grained than with "mere" Milestones.

So, are Projects something that supplements Milestones (or rather Milestones supplement Projects now?) or should I rather view Projects as a replacement of Milestones?

Where exactly do the Projects actually fall into the repository[-milestone]-issue hierarchy?

Sadly, GitHub's blog entry about the introduction of the Projects doesn't mention any relationship (https://github.com/blog/2256-a-whole-new-github-universe-announcing-new-tools-forums-and-features).

I somehow feel there is one, but I can't put a finger on it.

I'm wondering the exact same thing. Here is what I came up with.

First, let's review the main similarities and differences:

• An issue can belong to multiple Projects, but only one Milestone.
• Projects are never complete. There is no progress bar, or deadline. Projects have no progress bar or deadline (they do now, though it is hidden inside the project's menu as a "Track project progress" checkmark, and there's no percentage calculation of progress), but can now be closed (as pointed out by @Sheen)
• Milestones on the other hand have all that, but lack any form of organization. An issue is either in a milestone, or isn't. (They can be ordered as pointed out by @Nick McCurdy)
• Issues can be filtered by Milestone, but not by Project. As pointed out by @cmonkey, issues can now be filtered by Project as well as Milestone.
• Projects can contain Notes (which can be converted as issues) so it doesn't pollute the issue tracker with vague ideas
• A Project can span over multiple Milestones, and a Milestone can contains parts of different Projects.
• An Organization can have Projects as well. These projects can include tickets from any repository in the organization, which makes it quite useful.

So the way I see it, is that Projects are a completely separate way to visualize and organize your work on an higher level (think "project management", multiple teams, multiple repository, etc.), while Milestones are a way to organize your deadlines and releases on a more basic level (think "release management", "versions", etc.). With this in mind, it makes sense that an issue only belongs to one Milestone (it's only released or pushed to production once) but can be part of different Projects.

I'm sure they are other ways to look at it though, and I'm interested to hear other opinions.

Edit December 2017

Some time ago, after working with Milestones and Projects for over a year, I realized there is another important aspect I had completely overlooked.

• Milestones is a tool for Scrum methodology. Milestones are good for timeboxed iterations and working in sprints with batches of issues.
• Projects is a tool for Kanban methodology. Projects are good for continuous delivery and steady flow of work.